Updated conf to include excel files. Added new output files to macs2 job & module.

chipathlon/conf.py

@@ -47,7 +47,8 @@ file_extensions = {
     "quality": ["quality"],
     "qc": ["qc"],
     "pdf": ["pdf"],
-    "ccscore": ["ccscore"]
+    "ccscore": ["ccscore"],
+    "xls": ["xls"]
 }
 
 # list of resources that can be specified per job (step) in

chipathlon/jobs/modules/peak_call.yaml

@@ -49,7 +49,11 @@ peak_call:
               type: argument
         additional_inputs: null
         outputs:
-          - results.narrowPeak:
+          - peaks.narrowPeak:
+              type: file
+          - peaks.xls:
+              type: file
+          - summits.bed:
               type: file
     - sort_awk_sort_peaks:
         inputs:

chipathlon/jobs/params/macs2_callpeak.yaml

@@ -10,6 +10,10 @@ macs2_callpeak:
   outputs:
     - bed:
         type: file
+    - xls:
+        type: file
+    - bed:
+        type: file
   command: macs2
   arguments:
     - callpeak:

chipathlon/jobs/scripts/db_save_bed.py → chipathlon/jobs/scripts/db_save_result.py

@@ -5,8 +5,15 @@ parser = argparse.ArgumentParser(description="Insert a bed file into the databas
 parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
 parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.")
 parser.add_argument("-h", "--host", dest="host", required=True, help="Database host.")
-parser.add_argument("-f", "--file", dest="file", required=True, help="Path to bed file.")
+parser.add_argument("-f", "--file", dest="file", required=True, help="Path to result file.")
 parser.add_argument("-c", "--controls", dest="control_ids", required=True, nargs="+", help="List of control ids.")
 parser.add_argument("-e", "--experiments", dest="experiment_ids", required=True, nargs="+", help="List of experiment/signal ids.")
 parser.add_argument("-a", "--additional", dest="additional")
+parser.add_argument("-t", "--type", dest="type", required=True, help="Type of result file to save [bed, peak]")
 args = parser.parse_args()
+
+mdb = chipathlon.db.MongoDB(args.host, args.username, args.password)
+if args.type() == "bed":
+    mdb.save_bed(args.f, args.c, args.e, {})
+elif args.type() == "peak":
+    mdb.save_peak(args.f, args.c, args.e, {})